Quite.  In the Suśruta Project's edition we've gone with geminated consonants (karmma, karttā) and some other odd sandhi choices (evaṅ guṇam) because they are sanctioned by Pāṇini.  It's going to make our edition a bit odd for readers who are used to smoothed-out Sanskrit.  But it's grammatically correct.  And that's another editorial assumption: we assume that our author(s) know grammar.  That can also be tricky, if we think there are maybe some dialectical features appearing.  Luckily, the SS is a good example of classical Sanskrit.  Separating error from dialect or language drift, the BHS problem, is extra challenging.

Best,
Dominik

On Fri, 24 Mar 2023 at 21:39, Harry Spier <vasishtha.spier@gmail.com> wrote:
Point taken Dominik. You wrote:
 One has two files.  The first is the diplomatic transcription (karmma, vindu, adhiṣṭāna).  The second is whatever one wants it to be, but it's interpretative or normalized.

I think another reason, in addition to all the reasons you gave for what you suggest. I.e.  "first is the diplomatic transcription"  and only then to create a "normalized" file, is that deciding whats normal is sometimes a judgement call . There may be more than one norm. For example:
Monier-Williams dictionary has pattra and chattra but Apte's dictionary has patra and chatra .

Harry Spier